TABLE S1. Data characterized for this study.
rDNA 3
- -
Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2
Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878.
TABLE S2. Lineages based on Patterson 1999 with updates from Adl et al., 2005. Lineages Clade Genes Lineages Clade Genes Acanthamoebidae Amoebozoa 15 Nucleariidae Opisthokonta 5 Acantharea Rhizaria 1 Opisthokont Opisthokonta 16 Allantion Rhizaria 1 Oxymonadida Excavata 5 Allas Rhizaria 1 Parabasalids Excavata 16 Alveolates Alveolates 16 Paradinium Rhizaria 1 Ancyromonas* - 5 Paramonas Stramenopiles 1 Apusomonads - 6 Paramyxea - 1 Breviata - 12 Pelomyxa Amoebozoa 2 Centroheliozoa - 7 Phaeodarea Rhizaria 1 Cercomonadida Rhizaria 10 Phalansterium Amoebozoa 2 Chlamydomyxa Stramenopiles 1 Plamsmodiophorida Rhizaria 4 Chlorarachniophytes Rhizaria 14 Pleurostomum Excavata 1 Collodictyonidae - 1 Polycystinea Rhizaria 2 Cryothecomonas Rhizaria 1 Proleptomonas Rhizaria 4 Cryptomonads Cryptomonads 10 Red algae Red algae 14 Desmothoracids Rhizaria 2 Soginia Excavata 5 Dimorphid Rhizaria 4 Stephanopogon Excavata 5 Ebriid Rhizaria 1 Sticholonche Rhizaria 1 Ellobiopsids Alveolates 1 Stramenopiles Stramenopiles 16 Entamoebidae Amoebozoa 16 Telonema - 4 Euglenozoa Excavata 16 Thaumatomonads Rhizaria 4 Euglyphida Rhizaria 4 Theratromyxa Rhizaria 1 Eumycetozoa Amoebozoa 16 Trichosphaerium Amoebozoa 4 Flabellinea Amoebozoa 2 Trimastix Excavata 16 Foraminifera Rhizaria 10 Tubulinea Amoebozoa 14 Diplomonadida Excavata 16 Vampryellidae Rhizaria 1 Carpediemonas Excavata 5 Viridaeplantae Viridaeplantae 16 Glaucophytes Glaucophytes 16 Xenophyophores Rhizaria 1 Gromia Rhizaria 3 Actinophryids Stramenopiles Gymnophrea Rhizaria 5 Biomyxa - Haplosporidia Rhizaria 2 Caecitellus Stramenopiles Haptophytes Haptophytes 15 Coelosporidium - Heterolobosea Excavata 16 Copromyxids - Hyperamoeba Amoebozoa 4 Discocelis Stramenopiles Jakobids Excavata 14 Fonticula - Kathablepharids Cryptomonads 7 Gymnosphaerida - Leukarachnion Stramenopiles 4 Komokiacea - Malawimonas Excavata 15 Luffisphaera - Mastigamoebidae Amoebozoa 16 Nephridiophagids Opisthokonta Mesomycetozoa Opisthokonta 15 Phagodinium - Metopion Rhizaria 1 Pseudodendromonads Stramenopiles Metromonas Rhizaria 1 Pseudospora - Ministeria Opisthokonta 8 Retortamonads Excavata Multicilia Amoebozoa 1 Spironemidae - These eukaryotic lineages, defined by ultrastructural identities (Patterson, 1999), have proven robust in analyses with multiple datatypes (Parfrey et al. 2006; Simpson and Patterson 2006; Yoon et al. 2008). The lone exception is ‘ramicristates’, which is now divided between Amoebozoa and Rhizaria. Thus, lineages within Amoebozoa and Euglyphida are based on the classification of Adl et al. 2005. Clade = Higher-level grouping into which lineage has been subsummed (e.g. (Pawlowski and Burki 2009; Simpson and Patterson 2006)). Genes = number of genes in this study. *The identity of this taxon was recently clarified and Planomonas is a junior synonym (Heiss et al. 2010). See Table S4 for more detail on genes included in analysis. TABLE S3. Protein-coding genes used in this study Homolo Gene name Alternate gene names Gene IDs Taxa
Grf4 (General regulatory factor4) tyrosine 3-monooxygenase/tryptophan 14-3-3 5-monooxygenase activation protein 100743 87 40S 40S ribosomal protein S4 90857 82 Actin actin, beta 110648 197 Atub tubulin, alpha 4a 68496 158 Btub tubulin, beta 4 55952 161 eukaryotic translation elongation factor 1 Ef1α alpha 1 105313 98 EF2 eukaryotic translation elongation factor 2 100816 86 Enolase enolase 1 68183 84 Grc5 60S ribosomal protein L10 68830 87 Hsp70cyt heat shock 70kDa protein 8 68524 94 Hsp90 heat shock protein 90kDa alpha (cytosolic) 74306 130 methionine adenosyltransferase II alpha, MetK S-adenosylmethionine synthetase 38112 77 Rps22a Rps15a (ribosomal protein S15A) 111120 77 ribosomal protein S23 Rps23a 40S ribosomal protein S23 799 86 Tsec61 Sec61 alpha 1 subunit 55537 77
Gene: The protein-coding genes included in this study, with the abbreviation corresponding to the data matrix. Alternate gene names are taken from HomoloGene. HomoloGene IDs are from www.ncbi.nlm.nih.gov/HomoloGene/. Taxa: number of taxa with protein-coding gene sequences in our analysis. TABLE S4. Details on individual genes by taxa
Lineage based on
Patterson 1999,
Supergroup Taxon
rDNA 3
- updated with Adl et. -
3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Amoebozoa Entamoebidae Entamoeba histolytica 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Amoebozoa Eumycetozoa Dictyostelium discoideum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Phreatamoeba balamuthi Amoebozoa Mastigamoebidae (Mastigamoeba) 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Glaucophytes Cyanophora paradoxa 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Arabidopsis thaliana 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Ginkgo biloba 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Oryza sativa 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Archaeplastida’ Viridaeplantae Physcomitrella patens 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates Cryptosporidium parvum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates Paramecium tetraurelia 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates Plasmodium berghei 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates Tetrahymena thermophila 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates Toxoplasma gondii 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Alveolates Theileria parva 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Stramenopiles Phaeodactylum tricornutum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 ‘Chromalveolata’ Stramenopiles Thalassiosira pseudonana 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Euglenozoa Leishmania major 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Euglenozoa Trypanosoma brucei 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Diplomonadida Giardia lamblia ATCC 50803 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Heterolobosea Naegleria gruberi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Jakobids Seculamonas ecuadoriensis' 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Excavata Parabasalids Trichomonas vaginalis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Trimastix pyriformis ATCC Excavata Trimastix 50562 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Caenorhabditis elegans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Candida albicans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Ciona intestinalis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Drosophila melanogaster 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Gallus gallus 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Homo sapiens 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Saccharomyces cerevisiae 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Schizosaccharomyces pombe 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Opisthokonta Opisthokonta Nematostella vectensis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 Amoebozoa Acanthamoebidae Acanthamoeba castellanii 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Amoebozoa Eumycetozoa Physarum polycephalum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Archaeplastida’ Viridaeplantae Chlamydomonas reinhardtii 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Archaeplastida’ Viridaeplantae Micromonas pusilla 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Archaeplastida’ Viridaeplantae Volvox carteri 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Alveolates Perkinsus marinus 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Haptophytes Emiliania huxleyi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Haptophytes Isochrysis galbana 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Stramenopiles Aureococcus anophagefferens 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 ‘Chromalveolata’ Stramenopiles Phytophthora infestans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Excavata Jakobids Reclinomonas americana 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Excavata Malawimonas Malawimonas jakobiformis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Branchiostoma floridae 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Monosiga brevicollis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Opisthokonta Opisthokonta Phanerochaete chrysosporium 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Strongylocentrotus purpuratus 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Opisthokonta Ustilago maydis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Opisthokonta Mesomycetozoa Capsaspora owczarzaki 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 15 Amoebozoa Tubulinea Hartmannella vermiformis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Red algae Porphyra yezoensis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Viridaeplantae Mesostigma viride 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Viridaeplantae Welwitschia mirabilis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Chromalveolata’ Alveolates Alexandrium tamarense 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Excavata Euglenozoa Euglena gracilis 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Excavata Euglenozoa Diplonema papillatum 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Excavata Euglenozoa Euglena longa 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Opisthokonta Opisthokonta Encephalitozoon cuniculi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Opisthokonta Opisthokonta Schistosoma mansoni 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Opisthokonta Mesomycetozoa Sphaeroforma arctica 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 Rhizaria Chlorarachniophyta Bigelowiella natans 1 1 1 1 1 1 1 1 1 1 1 1 1 1 14 ‘Archaeplastida’ Glaucophytes Glaucocystis nostochinearum 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Archaeplastida’ Red algae Chondrus crispus 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Haptophytes Pavlova lutheri 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Haptophytes Prymnesium parvum 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Stramenopiles Blastocystis hominis 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Excavata Diplomonadida Spironucleus vortens 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Excavata Heterolobosea Sawyeria marylandensis 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Excavata Oxymonadida Streblomastix strix 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Allomyces macrogynus ATCC Opisthokonta Opisthokonta 38327 1 1 1 1 1 1 1 1 1 1 1 1 1 13 Opisthokonta Opisthokonta Aplysia californica 1 1 1 1 1 1 1 1 1 1 1 1 1 13 ‘Chromalveolata’ Alveolates Nyctotherus ovalis 1 1 1 1 1 1 1 1 1 1 1 1 12 Excavata Diplomonadida Spironucleus barkhanus 1 1 1 1 1 1 1 1 1 1 1 1 12 Excavata Jakobids Jakoba libera 1 1 1 1 1 1 1 1 1 1 1 1 12 Opisthokonta Opisthokonta Mnemiopsis leidyi 1 1 1 1 1 1 1 1 1 1 1 1 12 Opisthokonta Opisthokonta Oscarella carmela 1 1 1 1 1 1 1 1 1 1 1 1 12 Opisthokonta Opisthokonta Spizellomyces punctatus 182 1 1 1 1 1 1 1 1 1 1 1 1 12 Other Breviata Breviata anathema 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Alveolates Entodinium caudatum 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Alveolates Karenia brevis 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Cryptophyta Guillardia theta 1 1 1 1 1 1 1 1 1 1 10 Opisthokonta Opisthokonta Capitella capitata 1 1 1 1 1 1 1 1 1 1 1 11 Opisthokonta Mesomycetozoa Amoebidium parasiticum 1 1 1 1 1 1 1 1 1 1 1 11 ‘Chromalveolata’ Alveolates Eimeria tenella 1 1 1 1 1 1 1 1 1 1 10 ‘Chromalveolata’ Alveolates Chilodonella uncinata 1 1 1 1 1 1 1 1 1 1 10 Heteromita (chimera of H. globosa and H sp. ATCC PRA- Rhizaria Cercomonadida 74) 1 1 1 1 1 1 1 1 1 1 10 Rhizaria Foraminifera Reticulomyxa filosa 1 1 1 1 1 1 1 1 1 1 10 ‘Archaeplastida’ Green algae Acetabularia acetabulum 1 1 1 1 1 1 1 1 1 9 Opisthokonta Opisthokonta Glomus intraradices 1 1 1 1 1 1 1 1 1 9 Excavata Euglenozoa Bodo saltans 1 1 1 1 1 1 1 1 8 Opisthokonta Ministeria Ministeria vibrans 1 1 1 1 1 1 1 1 8 ‘Archaeplastida’ Red algae Cyanidioschyzon merolae 1 1 1 1 1 1 1 7
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum ‘Chromalveolata’ Stramenopiles Apodachlya brachynema 1 1 1 1 1 1 1 7 ‘Chromalveolata’ Stramenopiles Heterosigma akashiwo 1 1 1 1 1 1 1 7 Excavata Jakobids Andalucia incarcerata 1 1 1 1 1 1 1 7 Excavata Jakobids Andalucia godoyi 1 1 1 1 1 1 1 7 Other Kathablepharids Leucocryptos marina 1 1 1 1 1 1 1 7 Rhizaria incertae sedis Corallomyxa tenera 1 1 1 1 1 1 1 7 Amoebozoa incertae sedis Arachnula sp. ATCC 50593 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates Sarcocystis neurona 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates Heterocapsa rotundata 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates Oxyrrhis marina 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates Gregarina niphandrodes 1 1 1 1 1 1 6 ‘Chromalveolata’ Cryptophyta Goniomonas truncata 1 1 1 1 1 1 6 Excavata Diplomonadida Hexamita inflata 1 1 1 1 1 1 6 Monocercomonas sp. ATCC Excavata Parabasalids 50210 1 1 1 1 1 1 6 Opisthokonta Opisthokonta Salpingoeca amphoridium 1 1 1 1 1 1 6 Opisthokonta Mesomycetozoa Corallochytrium limacisporum 1 1 1 1 1 1 6 Apusomonas proboscidea Other Apusomonads CCAP 1905/1 1 1 1 1 1 1 6 Other Centroheliozoa Raphidiophrys contractilis 1 1 1 1 1 1 6 ‘Chromalveolata’ Alveolates Crypthecodinium cohnii 1 1 1 1 1 5 ‘Chromalveolata’ Alveolates Stylonychia lemnae 1 1 1 1 1 5 ‘Chromalveolata’ Stramenopiles Mallomonas rasilis 1 1 1 1 1 5 ‘Chromalveolata’ Stramenopiles Phytophthora palmivora 1 1 1 1 1 5 Excavata Carpediemonas Carpediemonas membranifera 1 1 1 1 1 5 Monocercomonoides sp. Excavata Oxymonadida PA203 1 1 1 1 1 5 Excavata Parabasalids Trichonympha agilis 1 1 1 1 1 5 ATCC 50646 (“Soginia Excavata Soginia anisocystis”) 1 1 1 1 1 5 Excavata Stephanopogon Stephanopogon apogon 1 1 1 1 1 5 Nuclearia simplex CCAP Opisthokonta Nucleariidae 1552/4 1 1 1 1 1 5 Opisthokonta Opisthokonta Rhizopus microsporus 1 1 1 1 1 5 Opisthokonta Opisthokonta Diaphanoeca grandis 1 1 1 1 1 5 Opisthokonta Opisthokonta Aphrocallistes vastus 1 1 1 1 1 5 Ancyromonas micra ATCC Other Ancyromonas 50267 1 1 1 1 1 5 Rhizaria Cercomonadida Massisteria marina 1 1 1 1 1 5 Rhizaria Gymnophrea Gymnophrys sp. ATCC 50923 1 1 1 1 1 5 Hyperamoeba sp. ATCC PRA- Amoebozoa Hyperamoeba 39 1 1 1 1 4 Amoebozoa incertae sedis Parvamoeba monoura 1 1 1 1 4 Trichosphaerium sp. ATCC Amoebozoa Trichosphaerium 40318 1 1 1 1 4 Amoebozoa Tubulinea Nolandella sp. ATCC PRA-27 1 1 1 1 4 Amoebozoa Tubulinea Rhizamoeba sp. ATCC 50933 1 1 1 1 4 ‘Archaeplastida’ Green algae Coleochaete scutata 1 1 1 1 4 ‘Archaeplastida’ Green algae Chlorella vulgaris 1 1 1 1 4 ‘Chromalveolata’ Alveolates Prorocentrum minimum 1 1 1 1 4
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum ‘Chromalveolata’ Alveolates Kryptoperidinium foliaceum 1 1 1 1 4 ‘Chromalveolata’ Alveolates Blepharisma japonicum 1 1 1 1 4 ‘Chromalveolata’ Alveolates Noctiluca scintillans 1 1 1 1 4 ‘Chromalveolata’ Cryptophyta Storeatula sp. CCMP1868 1 1 1 1 4 ‘Chromalveolata’ Cryptophyta Chroomonas mesostigmatica 1 1 1 1 4 ‘Chromalveolata’ Haptophytes Chrysochromulina polylepis 1 1 1 1 4 ‘Chromalveolata’ Leukarachnion Leukarachnion sp. 1 1 1 1 4 ‘Chromalveolata’ Stramenopiles Pelagomonas calceolata 1 1 1 1 4 ‘Chromalveolata’ Stramenopiles Thraustochytrium striatum 1 1 1 1 4 Excavata Euglenozoa Entosiphon sulcatum 1 1 1 1 4 Excavata Euglenozoa Rhynchopus sp. ATCC 50226 1 1 1 1 4 Excavata Heterolobosea Acrasis rosea 1 1 1 1 4 Excavata Heterolobosea Percolomonas cosmopolitus 1 1 1 1 4 Excavata Parabasalids Holomastigotoides mirabile 1 1 1 1 4 Excavata Trimastix Trimastix marina 1 1 1 1 4 other Telonema Telonema antarcticum 1 1 1 1 4 other Telonema Telonema subtile 1 1 1 1 4 Cercomonas sp. ATCC PRA- Rhizaria Cercomonadida 21 1 1 1 1 4 Rhizaria Cercomonadida Bodomorpha minima 1 1 1 1 4 Rhizaria Dimorphid Dimorpha sp. ATCC PRA-54 1 1 1 1 4 Rhizaria Euglyphida Capsellina sp 1 1 1 1 4 Rhizaria Foraminifera Ovammina opaca 1 1 1 1 4 Rhizaria Plamsmodiophorida Plasmodiophora brassicae 1 1 1 1 4 Rhizaria Proleptomonas Proleptomonas faecicola 1 1 1 1 4 Rhizaria Thaumatomonads Thaumatomonas seravini 1 1 1 1 4 Amoebozoa Eumycetozoa Polysphondylium violaceum 1 1 1 3 Amoebozoa Tubulinea Arcella hemisphaerica 1 1 1 3 Amoebozoa Tubulinea Amoeba proteus 1 1 1 3 ‘Chromalveolata’ Alveolates Loxodes striatus 1 1 1 3 ‘Chromalveolata’ Alveolates Metopus palaeformis 1 1 1 3 ‘Chromalveolata’ Alveolates Peridinium willei 1 1 1 3 ‘Chromalveolata’ Alveolates Euplotes octocarinatus 1 1 1 3 ‘Chromalveolata’ Alveolates Monocystis agilis 1 1 1 3 ‘Chromalveolata’ Alveolates Symbiodinium sp. AP309 1 1 1 3 ‘Chromalveolata’ Stramenopiles Nitzschia thermalis 1 1 1 3 ‘Chromalveolata’ Stramenopiles Labyrinthula sp. N12 1 1 1 3 Excavata Euglenozoa Cryptobia helicis 1 1 1 3 Excavata Euglenozoa Rhynchobodo sp. ATCC 50359 1 1 1 3 Excavata Diplomonadida Enteromonas hominis 1 1 1 3 Excavata Diplomonadida Trimitus sp. TRION 1 1 1 3 Excavata Oxymonadida Dinenympha exilis 1 1 1 3 Excavata Oxymonadida Pyrsonympha grandis 1 1 1 3 Opisthokonta Opisthokonta Trachipleistophora hominis 1 1 1 3 Opisthokonta Opisthokonta Stephanoeca diplocostata 1 1 1 3 Rhizaria Chlorarachniophyta Gymnochlora stellata 1 1 1 3 Rhizaria Foraminifera Allogromia sp. 1 1 1 3 Rhizaria Foraminifera Rhabdammina cornuta 1 1 1 3
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Gromia (chimera of G. Rhizaria Gromia oviformis G. sp Antarctica) 1 1 1 3 Rhizaria incertae sedis Spongomonas ATCC 50405 1 1 1 3 Amoebozoa Eumycetozoa Arcyria denudata 1 1 2 Amoebozoa Eumycetozoa Stemonitis flavogenita 1 1 2 Amoebozoa Eumycetozoa Trichia persimilis 1 1 2 Amoebozoa Flabellinea Neoparamoeba perurans 1 1 2 Amoebozoa Flabellinea Pessonella sp. PRA-29 1 1 2 Amoebozoa Flabellinea Platyamoeba placida 1 1 2 Amoebozoa Flabellinea Dermamoeba algensis 1 1 2 Amoebozoa Flabellinea Mayorella sp. JJP-2003 1 1 2 Amoebozoa Pelomyxa Pelomyxa palustris 1 1 2 Amoebozoa Phalansterium Phalansterium solitarium 1 1 2 Amoebozoa Thecamoebida Thecamoeba similis 1 1 2 Amoebozoa Thecamoebida Sappinia pedata 1 1 2 Amoebozoa Tubulinea Chaos carolinense 1 1 2 Amoebozoa Tubulinea Glaeseria mira 1 1 2 Amoebozoa Tubulinea Hartmannella cantabrigiensis 1 1 2 Amoebozoa Tubulinea Heleopera sphagni 1 1 2 Amoebozoa Tubulinea Paraflabellula hoguae 1 1 2 ‘Archaeplastida’ Red algae Glaucosphaera vacuolata 1 1 2 ‘Archaeplastida’ Red algae Nemalionopsis shawii 1 1 2 ‘Archaeplastida’ Red algae Rhodosorus marinus 1 1 2 ‘Archaeplastida’ Red algae Stylonema alsidii 1 1 2 ‘Chromalveolata’ Alveolates Dinophyceae sp. 1 1 2 ‘Chromalveolata’ Cryptophyta Teleaulax acuta 1 1 2 ‘Chromalveolata’ Haptophytes Pleurochrysis carterae 1 1 2 ‘Chromalveolata’ Stramenopiles Costaria costata 1 1 2 ‘Chromalveolata’ Stramenopiles Fucus disticus 1 1 2 ‘Chromalveolata’ Stramenopiles Protoopalina japonica 1 1 2 Excavata Euglenozoa Petalomonas cantuscygni 1 1 2 Excavata Diplomonadida Trepomonas agilis 1 1 2 Excavata Oxymonadida Saccinobaculus ambloaxostylus 1 1 2 Opisthokonta incertae sedis Micronuclearia podoventralis 1 1 2 Opisthokonta Opisthokonta Oreochromis esculentus 1 1 2 Opisthokonta Opisthokonta Proterospongia choanojuncta 1 1 2 Batrachochytrium Opisthokonta Opisthokonta dendrobatidis 1 1 2 Opisthokonta Opisthokonta Boothiomyces macroporosum 1 1 2 Other Centroheliozoa Chlamydaster sterni 1 1 2 other Kathablepharids Katablepharis remigera 1 1 2 Rhizaria Chlorarachniophyta Lotharella globosa 1 1 2 Rhizaria Desmothoracids Clathrulina elegans 1 1 2 Rhizaria Desmothoracids Hedriocystis reticulata 1 1 2 Rhizaria Euglyphida Euglypha rotunda 1 1 2 Rhizaria Foraminifera Ammonia sp. T7 1 1 2 Rhizaria Foraminifera Amphisorus hemprichii 1 1 2 Rhizaria Foraminifera Globobulimina turgida 1 1 2 Rhizaria Foraminifera Astrammina rara 1 1 2
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Rhizaria Haplosporidia Bonamia ostreae 1 1 2 Rhizaria Haplosporidia Haplosporidium costale 1 1 2 Rhizaria Haplosporidia Haplosporidium louisiana 1 1 2 Rhizaria Haplosporidia Haplosporidium nelsoni 1 1 2 Rhizaria Haplosporidia Minchinia chitonis 1 1 2 Rhizaria Haplosporidia Urosporidium_crescens 1 1 2 Rhizaria incertae sedis Lecythium sp. 1 1 2 Rhizaria Plamsmodiophorida Sorosphaera_veronicae 1 1 2 Spongospora subterranea f. sp. Rhizaria Plamsmodiophorida subterranea 1 1 2 Rhizaria Polycystinea Collozoum inerme 1 1 2 Rhizaria Polycystinea Thalassicolla pellucida 1 1 2 Amoebozoa Acanthamoebidae Balamuthia mandrillaris 1 1 Amoebozoa Acanthamoebidae Comandonia operculata 1 1 Amoebozoa Acanthamoebidae Protacanthamoeba bohemica 1 1 Amoebozoa Entamoebidae Endolimax nana 1 1 Amoebozoa Eumycetozoa Didymium dubium 1 1 Amoebozoa Eumycetozoa Didymium iridis 1 1 Amoebozoa Eumycetozoa Didymium nigripes 1 1 Amoebozoa Eumycetozoa Lepidoderma carestianum 1 1 Amoebozoa Eumycetozoa Protophysarum phloiogenum 1 1 Pseudodidymium Amoebozoa Eumycetozoa cryptomastigophorum 1 1 Amoebozoa Eumycetozoa Symphytocarpus impexus 1 1 Amoebozoa Flabellinea Clydonella sp. ATCC 50884 1 1 Amoebozoa Flabellinea Korotnevella stella 1 1 Amoebozoa Flabellinea Lingulamoeba leei 1 1 Amoebozoa Flabellinea Platyamoeba plurinucleolus 1 1 Amoebozoa Flabellinea Vannella aberdonica 1 1 Amoebozoa Flabellinea Vannella miroides 1 1 Amoebozoa Flabellinea Vexillifera armata 1 1 Amoebozoa Flabellinea Vexillifera minutissima 1 1 Amoebozoa Flabellinea Cochliopodium spiniferum 1 1 Amoebozoa Flabellinea Platyamoeba stenopodia 1 1 Amoebozoa incertae sedis Filamoeba nolandi 1 1 Gephyramoeba sp. ATCC Amoebozoa incertae sedis 50654 1 1 Amoebozoa Mastigamoebidae Mastigamoeba simplex 1 1 Mastigamoeba sp. ATCC Amoebozoa Mastigamoebidae 50617 1 1 Amoebozoa Mastigamoebidae Mastigella commutans 1 1 Amoebozoa Multicilia Multicilia marina 1 1 Amoebozoa Tubulinea Amoeba leningradensis 1 1 Amoebozoa Tubulinea Centropyxis laevigata 1 1 Amoebozoa Tubulinea Chaos nobile 1 1 Amoebozoa Tubulinea Echinamoeba exundans 1 1 Amoebozoa Tubulinea Leptomyxa reticulata 1 1 Amoebozoa Tubulinea Paraflabellula reniformis 1 1 Amoebozoa Tubulinea Rhizamoeba saxonica 1 1 Amoebozoa Tubulinea Ripidomyxa sp. RP010 1 1
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Amoebozoa Tubulinea Saccamoeba limax 1 1 ‘Archaeplastida’ Glaucophytes Cyanoptyche gloeocystis 1 1 ‘Archaeplastida’ Red algae Bangiopsis subsimplex 1 1 ‘Archaeplastida’ Red algae Pterocladiella nana 1 1 ‘Archaeplastida’ Green algae Araucaria heterophylla 1 1 ‘Archaeplastida’ Green algae Chlorokybus atmophyticus 1 1 ‘Archaeplastida’ Green algae Closterium ehrenbergii 1 1 ‘Archaeplastida’ Green algae Cycas taitungensis 1 1 ‘Archaeplastida’ Green algae Elliptochloris sp. E20-d 1 1 ‘Archaeplastida’ Green algae Geminella minor 1 1 ‘Archaeplastida’ Green algae Halimeda macrophysa 1 1 ‘Archaeplastida’ Green algae Kirchneriella aperta 1 1 ‘Archaeplastida’ Green algae Koliella planctonica 1 1 ‘Archaeplastida’ Green algae Lunularia cruciata 1 1 ‘Archaeplastida’ Green algae Lycopodium tristachyum 1 1 ‘Archaeplastida’ Green algae Oltmannsiellopsis geminata 1 1 ‘Archaeplastida’ Green algae Raphidonema nivale 1 1 ‘Archaeplastida’ Green algae Tetraselmis kochiensis 1 1 ‘Archaeplastida’ Green algae Zygnema cylindricum 1 1 ‘Chromalveolata’ Alveolates Adelina dimidiata 1 1 ‘Chromalveolata’ Alveolates Aggregata octopiana 1 1 Amoebophrya sp. ex ‘Chromalveolata’ Alveolates Scrippsiella 1 1 ‘Chromalveolata’ Alveolates Blastodinium navicula 1 1 ‘Chromalveolata’ Alveolates Bursaria truncatella 1 1 ‘Chromalveolata’ Alveolates Chromera velia 1 1 ‘Chromalveolata’ Alveolates Colpodella sp. ATCC 50594 1 1 ‘Chromalveolata’ Alveolates Colpodidium caudatum 1 1 ‘Chromalveolata’ Alveolates Dinophysis acuminata 1 1 ‘Chromalveolata’ Alveolates Geleia fossata 1 1 ‘Chromalveolata’ Alveolates Gloeodinium viscum 1 1 ‘Chromalveolata’ Alveolates Hemidinium nasutum 1 1 ‘Chromalveolata’ Alveolates Ichthyodinium chabelardi 1 1 ‘Chromalveolata’ Alveolates Ophriocystis elektroscirrha 1 1 ‘Chromalveolata’ Alveolates Prorodon viridis 1 1 ‘Chromalveolata’ Alveolates Pyrocystis noctiluca 1 1 ‘Chromalveolata’ Alveolates Rhytidocystis polygordiae 1 1 Thoracosphaera heimii CCCM ‘Chromalveolata’ Alveolates 670 1 1 ‘Chromalveolata’ Alveolates Voromonas pontica 1 1 Chlamydomyxa ‘Chromalveolata’ Chlamydomyxa labyrinthuloides 1 1 ‘Chromalveolata’ Cryptophyta Chilomonas paramecium 1 1 ‘Chromalveolata’ Cryptophyta Chilomonas sp. M1303 1 1 ‘Chromalveolata’ Cryptophyta Hemiselmis rufescens 1 1 ‘Chromalveolata’ Ellobiopsids Thalassomyces fagei 1 1 ‘Chromalveolata’ Haptophytes Calcidiscus leptoporus 1 1 ‘Chromalveolata’ Haptophytes Corcontochrysis noctivaga 1 1 ‘Chromalveolata’ Haptophytes Phaeocystis pouchetii 1 1 ‘Chromalveolata’ Paramonas Paramonas globosa 1 1
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum ‘Chromalveolata’ Stramenopiles Blastocystis sp. H11 1 1 ‘Chromalveolata’ Stramenopiles Bolidomonas pacifica 1 1 ‘Chromalveolata’ Stramenopiles Cafeteria roenbergensis 1 1 ‘Chromalveolata’ Stramenopiles Chrysocapsa paludosa 1 1 ‘Chromalveolata’ Stramenopiles Ciliophrys infusionum 1 1 ‘Chromalveolata’ Stramenopiles Heterococcus pleurococcoides 1 1 ‘Chromalveolata’ Stramenopiles Hyphochytrium catenoides 1 1 ‘Chromalveolata’ Stramenopiles Nannochloropsis maritima 1 1 ‘Chromalveolata’ Stramenopiles Ochromonas danica 1 1 ‘Chromalveolata’ Stramenopiles Phaeomonas parva 1 1 ‘Chromalveolata’ Stramenopiles Phaeothamnion confervicola 1 1 ‘Chromalveolata’ Stramenopiles Picophagus flagellatus 1 1 ‘Chromalveolata’ Stramenopiles Pinguiochrysis pyriformis 1 1 ‘Chromalveolata’ Stramenopiles Schizocladia ischiensis 1 1 ‘Chromalveolata’ Stramenopiles Spumella elongata 1 1 ‘Chromalveolata’ Stramenopiles Wobblia lunata 1 1 Excavata Euglenozoa Astasia curvata 1 1 Excavata Euglenozoa Blastocrithidia culicis 1 1 Cryptoglena pigra CCAP Excavata Euglenozoa 1212/1 1 1 Excavata Euglenozoa Distigma gracile 1 1 Excavata Euglenozoa Eutreptia viridis 1 1 Excavata Euglenozoa Gyropaigne lefevrei 1 1 Excavata Euglenozoa Herpetomonas roitmani 1 1 Excavata Euglenozoa Lepocinclis spirogyroides 1 1 Excavata Euglenozoa Wallaceina brevicula 1 1 Excavata Diplomonadida Octomitus intestinalis 1 1 Excavata incertae sedis Dysnectes brevis 1 1 Excavata Heterolobosea Heteramoeba clara 1 1 Excavata Heterolobosea Monopylocystis visvesvarai 1 1 Excavata Heterolobosea Paravahlkampfia ustiana 1 1 Excavata Heterolobosea Psalteriomonas lanterna 1 1 Excavata Heterolobosea Tetramitus thermacidophilus 1 1 Excavata Heterolobosea Vahlkampfia avara 1 1 Excavata Heterolobosea Vahlkampfia damariscottae 1 1 Excavata Oxymonadida Oxymonas sp. NcOxA 1 1 Excavata Parabasalids Calonympha grassii 1 1 Excavata Parabasalids Deltotrichonympha operculata 1 1 Excavata Parabasalids Histomonas meleagridis 1 1 Excavata Parabasalids Hoplonympha sp. MO-2004-1 1 1 Excavata Parabasalids Joenia sp. KfJeA 1 1 Excavata Parabasalids Koruga bonita 1 1 Excavata Parabasalids Pentatrichomonoides scroa 1 1 Excavata Parabasalids Pseudotrypanosoma giganteum 1 1 Spirotrichonymphella sp. MO- Excavata Parabasalids 2004-1 1 1 Excavata Parabasalids Staurojoenina assimilis 1 1 Excavata Parabasalids Stephanonympha nelumbium 1 1 Excavata Parabasalids Teranympha mirabilis 1 1
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Excavata Pleurostomum Pleurostomum flabellatum 1 1 Excavata Stephanopogon Stephanopogon minuta 1 1 Opisthokonta Opisthokonta Sycon calcaravis 1 1 Opisthokonta Opisthokonta Monoblepharis macrandra 1 1 Opisthokonta Mesomycetozoa Amphibiothecum penneri 1 1 Opisthokonta Mesomycetozoa Dermocystidium percae 1 1 Opisthokonta Opisthokonta Eccrinidus flexilis 1 1 Opisthokonta Opisthokonta Palavascia patagonica 1 1 Opisthokonta Opisthokonta Taeniella carcini 1 1 Other Apusomonads Amastigomonas debruynei 1 1 Other Apusomonads Amastigomonas mutabilis 1 1 Other Centroheliozoa Acanthocystis nichollsi 1 1 Other Centroheliozoa Choanocystis rotundata 1 1 Other Centroheliozoa Heterophrys marina 1 1 Other Centroheliozoa Polyplacocystis symmetrica 1 1 Other Centroheliozoa Pterocystis foliacea 1 1 Other Centroheliozoa Raineriophrys erinaceoides 1 1 Other Centroheliozoa Sphaerastrum fockii 1 1 Other Collodictyonidae Diphylleia rotans 1 1 other Kathablepharids Hatena arenicola 1 1 Other Paramyxea Marteilioides chungmuensis 1 1 Rhizaria Acantharea Acanthometra sp. 1 1 Rhizaria Acantharea Amphiacon denticulatus 1 1 Rhizaria Acantharea Amphibelone anomala 1 1 Rhizaria Acantharea Arthracanthid 206 1 1 Rhizaria Acantharea Chaunacanthid 217 1 1 Rhizaria Acantharea Hexaconus serratus 1 1 Rhizaria Acantharea Symphyacanthid 211 1 1 Rhizaria Allantion Allantion sp. ATCC 50734 1 1 Rhizaria Allas Allas diplophysa 1 1 Rhizaria Cercomonadida Cercomonas agilis 1 1 Rhizaria Cercomonadida Neocercomonas jutlandica 1 1 Rhizaria Chlorarachniophyta Chlorarachnion reptans 1 1 Rhizaria Cryothecomonas Cryothecomonas longipes 1 1 Rhizaria Ebriid Ebria tripartita 1 1 Rhizaria Euglyphida Assulina seminulum 1 1 Rhizaria Euglyphida Corythion dubium 1 1 Rhizaria Euglyphida Cyphoderia ampulla 1 1 Rhizaria Euglyphida Pseudodifflugia cf. gracilis 1 1 Rhizaria Euglyphida Trinema lineare 1 1 Rhizaria Foraminifera Borelis schlumbergeri 1 1 Rhizaria Foraminifera Cribrothalammina alba 1 1 Rhizaria Foraminifera Eggerelloides scabrum 1 1 Rhizaria Foraminifera Trochammina hadai 1 1 Rhizaria Gymnophrea Gymnophrys cometa 1 1 Rhizaria Haplosporidia Mikrocytos mackini 1 1 Rhizaria incertae sedis Aurigamonas solis 1 1 Rhizaria Metopion Metopion fluens 1 1 Rhizaria Metromonas Metromonas simplex 1 1
Lineage based on
Patterson 1999,
rDNA 3
Supergroup Taxon
- -
updated with Adl et. 3 al., 2005 -
SSU 14 40S Actin Atub Btub Ef1a Ef2 Enolase Grc5 Hsp70cyt Hsp90 MetK Rps22a Rps23a Tsec61 Sum Rhizaria incertae sedis Filoreta marina 1 1 Rhizaria Paradinium Paradinium poucheti 1 1 Rhizaria Paradinium Paradinium sp. PaEu41 1 1 Rhizaria Phaeodarea Aulacantha scolymantha 1 1 Rhizaria Phaeodarea Aulosphaera trigonopa 1 1 Rhizaria Phaeodarea Challengeron diodon 1 1 Rhizaria Phaeodarea Coelodendrum_ramosissimum 1 1 Rhizaria Phaeodarea Conchellium capsula 1 1 Rhizaria Phaeodarea Protocystis xiphodon 1 1 Rhizaria Plamsmodiophorida Maullinia ectocarpii 1 1 Rhizaria Plamsmodiophorida Phagomyxa odontellae 1 1 Rhizaria Plamsmodiophorida Polymyxa betae 1 1 Rhizaria Polycystinea Acrosphaera sp. CR6A 1 1 Rhizaria Polycystinea Artostrobus sp. 2014 1 1 Rhizaria Polycystinea Didymocyrtis tetrathalamus 1 1 Rhizaria Polycystinea Eucyrtidium hexastichum 1 1 Rhizaria Polycystinea Larcopyle butschlii 1 1 Rhizaria Polycystinea Lithomelissa sp. 8012 1 1 Rhizaria Polycystinea Pseudocubus obeliscus 1 1 Rhizaria Polycystinea Pterocanium trilobum 1 1 Rhizaria Polycystinea Pterocorys zancleus 1 1 Rhizaria Polycystinea Siphonosphaera cyathina 1 1 Rhizaria Polycystinea Sphaerozoum punctatum 1 1 Rhizaria Polycystinea Spongaster tetras 1 1 Rhizaria Polycystinea Stylodictya sp. 8037 1 1 Rhizaria Polycystinea Styptosphaera sp. 2022 1 1 Rhizaria Polycystinea Tetrapyle octacantha 1 1 Rhizaria Sticholonche Sticholonche sp. JJP-2003 1 1 Rhizaria Thaumatomonads Protaspis grandis 1 1 Thaumatomastix sp. ATCC Rhizaria Thaumatomonads 50250 1 1 Rhizaria Theratromyxa Theratromyxa weberi 1 1 Vampyrellidae sp. Fritzlar- Rhizaria Vampryellid Werkel 1 1 Rhizaria Xenophyophores Xenophyophorea sp. BBL-2008 1 1
TABLE S5. Support for major clades from additional analyses comparing taxon and gene sets from other studies
Supported clades Hampl: 16 gene Yoon: 16 gene All: 4 gene
Opisthokonta 100 93 98 Rhizaria 100 100 89 SAR 95 100 nm Rhizaria + stramenopiles 80 93 nm Excavata 82 nm nm Amoebozoa 99 44 44 ‘Unikonta' 99 nm nm
Weak/unsupported hypotheses
‘Archaeplastida’ 32 nm nm ‘Chromalveloata' nm nm nm Cryptomonads + haptophytes na nm 16 Haptophytes + SAR 73 58 nm Alveolates + stramenopiles nm nm 25 Red algae + green algae 64 nm nm Red, Green, Glauco, Hapto, Crypt na nm nm
Dataset statistics Number of taxa 48 101 168 Number of lineages 19 26 46 % Missing data (characters) 21 39 11
Additional analyses with taxon selection based on recent published analyses to explore tradeoffs between taxon and gene sampling (see methods and Table 1 for more details). ‘Hampl: 16 gene’ and ‘Yoon: 16 gene’ includes all 16 genes with taxon selection based on Hampl et al. 2009 and
Yoon et al. 2008. ‘All: 4 gene’ is an analysis of four commonly sampled markers (actin, alpha tubulin, beta tubulin, and ssu-rDNA) and all of our taxa with at least 3 of these 4 genes. See
Figure S1j-l for individual trees. TABLE S6. Support for major clades from additional analyses that attempt to address EGT.
EGT EGT - -
Supported clades 5: non 3: non 3: caterp 7 gene 5: caterp 13 gene 5: caterp 9 gene 10:16 no HC
Opisthokonta 94 89 17 96 96 100 Rhizaria 100 81 29 98 nm 100 SAR nm 55 20 78 nm 100 Rhizaria + stramenopiles nm 28 18 67 nm 79 Excavata nm 27 02 56 nm 84 Amoebozoa nm nm 11 95 51 66 ‘Unikonta' nm nm 05 92 nm 57
Weak/unsupported hypotheses
‘Archaeplastida’ nm nm nm nm nm nm ‘Chromalveloata' nm nm nm nm nm na Cryptomonads + haptophytes nm nm nm nm nm na Haptophytes + SAR nm 57 17 73 31 na Alveolates + stramenopiles nm nm nm nm nm na Red algae + green algae nm nm nm nm nm 81 Red, Green, Glauco, Hapto, Crypt nm nm nm nm nm nm
Dataset statistics Number of taxa 77 91 91 90 111 83 Number of lineages 23 26 25 25 30 24 % Missing data (characters) 8 11 16 17 19 20
Additional analyses to further explore the impact of subsampling genes and taxa to account for EGT on clade support (see methods and Table 1 for more details). ‘5: non-EGT’ and ‘3: non- EGT’ include taxa with at least 5 of 7 (or 3 of 7) candidate genes not likely to have originated by EGT in BLAST analysis. ‘3: caterp 7 gene’ includes taxa with at least 3 of 7 genes identified as largest concordant gene set by Concaterpillar, plus ssu-rDNA. ‘5: caterp 13 gene’ includes taxa with at least 5 of 13 genes; three excluded genes were not concordant with any others according to Concaterpillar. ‘5: caterp 9 gene’ includes taxa with at least 5 of 9 genes; gene sampling is largest concordant gene set identified by Concaterpillar run on only photosynthetic taxa. ‘10:16 no HC’ is the 10:16 dataset with haptophytes and cryptomonads removed. See Figure S1m-r for individual trees. Na= not able to evaluate. TABLE S7. Topology tests of ‘Archaeplastida’, ‘Chromalveolata’ and ‘Chromista’ hypotheses
Topology au kh sh wkh wsh np bp pp mb Most likely 0.811 0.781 0.924 0.781 0.927 0.779 0.780 1 ‘Archaeplastida’ monophyletic 0.226 0.219 0.359 0.219 0.324 0.216 0.216 <0.001 0 ‘Chromalveolata’ monophyletic 0.007 0.005 0.019 0.005 0.009 0.004 0.004 <0.001 0 ‘Chromista’ monophyletic <0.001 <0.001 <0.001 <0.001 <0.001 <0.001 <0.001 <0.001 0
Topology test on 10:16 dataset to assess alternative hypotheses. Topology tests p-values for approximately unbiased test (au), Kishino–Hasegawa test (kh) , Shimodaira–Hasegawa test (sh), weighted Kishino–Hasegawa test (skh) , weighted Shimodaira–Hasegawa test (wsh) . Non- parametric bootstrap probability (np) calculated from multiscale bootstrap, bootstrap probability (bp) calculated in the non-multiscale manner, Bayesian posterior probability (pp) calculated by Bayesian information-criterion approximation. The number of trees consistent with the given hypotheses (mb) in the 10,756 output trees of Bayesian analysis after stationarity. Results in bold significantly reject monophyly. All analyses except mb from Consel (Shimodaira and Hasegawa, 2001). TABLE S8. Position of unplaced ‘orphan’ lineages
Taxon Sistergroup Analysis BS taxon sistergroup analysis BS Ancyromonas Opisthokonta 4: 16 54 Centroheliozoa Haptophytes 6: 16 29 Ancyromonas Micronuclearia all: 16 27 Centroheliozoa Red algae 4: 16 26 Ancyromonas in Rhizaria 3: 15 3 Centroheliozoa Entamoebidae all: 16 5 Ancyromonas Micronuclearia all: 15 20 Centroheliozoa Breviata 5: 15 9 Ancyromonas Breviata all: 4 gene 26 Centroheliozoa Breviata 3: 15 7 Apusomonads Opisthokonta 6: 16 98 Centroheliozoa Breviata all: 15 11 Apusomonads Opisthokonta 4: 16 89 Centroheliozoa Red algae all: 4 gene 79 Apusomonads Opisthokonta all: 16 12 Centroheliozoa Red algae 5: caterp 9 39 Apusomonads Opisthokonta 5: 15 99 Diphylleia Entamoebidae all: 16 2 Apusomonads Opisthokonta 3: 15 65 Kathablepharids Cryptomonads 6: 16 85 Apusomonads Opisthokonta all: 15 9 Kathablepharids Cryptomonads 4: 16 57 Apusomonads Opisthokonta all: 4 gene 99 Kathablepharids Cryptomonads all: 16 56 Apusomonads Opisthokonta 5: caterp 9 96 Kathablepharids Cryptomonads 5: 15 66 Breviata Opisthokonta 10: 16 17 Kathablepharids Haptophytes 3: 15 27 Breviata Centroheliozoa 6: 16 8 Kathablepharids Haptophytes all: 15 32 Breviata Amoebozoa 4: 16 8 Kathablepharids Cryptomonads all: 4 gene 66 Breviata Entamobidae all: 16 2 Kathablepharids Cryptomonads 5: caterp 9 86 Breviata Opisthokonta 9: 15 21 Micronuclearia Ancyromonas all: 16 27 Breviata Centroheliozoa 5: 15 9 Micronuclearia Ancyromonas all: 15 20 Breviata Centroheliozoa 3: 15 7 Mikrocytos in Euglenozoa all: 16 34 Breviata Centroheliozoa all: 15 11 Paramyxea Trichosphaerium all: 16 72 Breviata Ancyromonas all: 4 gene 26 Telonema Green algae 4: 16 25 Breviata Andalucia 5: caterp 9 3 Telonema Green algae all: 16 24 Breviata Opisthokonta 3: EGT 18 Telonema Green algae 3: 15 27 Breviata Malawimonas 3: caterp 7 29 Telonema Green algae all: 15 25 Telonema Stramenopiles all: 4 gene 32
We examined the position of unplaced lineages across our analyses. Our analysis reveals strongly supported sistergroup relationships for two previously unplaced lineages, apusomonads and kathablepharids. The sistergroup relationship of apusomonads + Opisthokonta is strongly supported across analyses. The relationship between kathablepharids and cryptomonads is recovered in all but one analysis; in all:15 cryptomonads are sister to the kathablepharid+haptophyte clade. In addition, Telonema consistently branches with green algae but with low support. The remaining lineages have yet to find stable homes, as evidenced by varying sistergroups and low support. BS: Bootstrap values calculated from analyses described in Tables 1 and S6.
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